Contacts of the strand formed by residues 2218 - 2225 (chain C) in PDB entry 4ILG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL2218 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2182C VAL* 3.5 15.5 - - + +
2184C VAL* 3.9 25.4 - - + -
2211C SER* 3.3 3.3 - - - -
2212C ALA* 3.1 32.0 + - + +
2215C HIS* 3.3 38.0 + - + +
2217C LYS* 1.3 78.4 - - - +
2219C LYS* 1.3 62.6 + - - +
2220C GLU* 3.6 13.8 + - + +
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Residues in contact with LYS2219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2181C ASN* 4.1 19.7 - - - +
2182C VAL 2.8 10.7 + - - +
2183C TYR* 3.4 36.6 - - + +
2184C VAL 2.9 25.0 + - - -
2210C MET 3.9 3.4 - - - -
2211C SER* 2.9 31.8 + - - +
2216C PRO 3.6 13.8 + - - +
2217C LYS 4.3 7.0 - - - +
2218C VAL* 1.3 69.9 - - - +
2220C GLU* 1.3 62.2 + - - +
2221C ILE* 3.7 1.2 + - - +
2254C GLU* 3.0 33.2 + - - +
2256C LEU* 4.4 13.5 - - + -
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Residues in contact with GLU2220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2184C VAL* 4.0 13.5 - - + +
2209C GLY* 3.2 4.7 - - - -
2210C MET 2.9 38.8 + - - +
2212C ALA* 4.7 17.0 - - + +
2218C VAL* 4.3 21.8 - - + +
2219C LYS* 1.3 73.0 - - - +
2221C ILE* 1.3 63.2 + - - +
2222C LYS* 3.5 21.7 + - - +
2256C LEU* 4.1 0.8 - - - +
2345C ILE* 4.3 34.2 - - + +
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Residues in contact with ILE2221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2183C TYR* 4.8 8.1 - - + -
2184C VAL 3.0 24.8 + - - +
2185C LEU* 3.8 29.8 - - + -
2186C PRO* 3.1 25.5 - - + +
2189C LEU* 4.1 18.8 - - + -
2207C ILE* 4.0 35.7 - - + -
2208C TYR 3.7 10.1 - - - +
2219C LYS 4.7 2.7 - - - +
2220C GLU* 1.3 71.3 - - - +
2222C LYS* 1.3 61.8 + - - +
2223C THR 4.2 3.8 - - - +
2224C VAL* 4.7 0.4 - - + -
2256C LEU* 3.8 19.3 - - + -
2291C ILE* 4.2 10.1 - - + -
2339C LEU* 5.2 0.4 - - + -
2345C ILE* 4.5 3.8 - - - +
2346C THR 5.3 0.5 - - - +
2347C GLY* 4.9 0.2 - - - -
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Residues in contact with LYS2222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2189C LEU* 4.4 2.0 - - - -
2208C TYR 2.8 7.8 + - - +
2209C GLY* 3.6 17.0 - - - -
2210C MET* 3.7 32.1 - - + +
2220C GLU* 3.8 25.8 + - + +
2221C ILE* 1.3 75.7 - - - +
2223C THR* 1.3 70.3 + - - +
2253C LEU* 4.0 12.1 - - + -
2346C THR 5.3 4.3 - - - +
2347C GLY* 3.2 9.7 - - - -
2348C ASN* 2.9 25.5 + - - +
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Residues in contact with THR2223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2189C LEU* 4.7 0.4 - - - -
2206C PHE 4.1 0.2 - - - +
2207C ILE* 3.6 2.1 - - - -
2208C TYR* 2.8 36.4 + - + +
2221C ILE* 3.8 2.3 - - - +
2222C LYS* 1.3 85.4 - - - +
2224C VAL* 1.3 73.0 + - - +
2225C VAL* 4.2 5.8 - - + -
2244C ILE* 5.6 0.2 - - + -
2253C LEU* 4.1 19.8 - - + +
2348C ASN* 2.7 28.4 + - - +
2350C ILE* 3.7 36.6 - - + +
2376C TYR* 5.2 2.2 - - + -
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Residues in contact with VAL2224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2185C LEU* 5.2 3.4 - - + -
2189C LEU* 3.7 31.6 - - + +
2193C PHE* 4.7 9.0 - - + -
2205C ALA* 3.5 26.5 - - + -
2206C PHE 3.4 5.2 - - - +
2207C ILE* 4.1 17.5 - - + -
2221C ILE* 4.7 2.0 - - + -
2223C THR* 1.3 74.8 - - - +
2225C VAL* 1.3 64.6 + - - +
2226C LEU* 4.7 0.9 - - + +
2259C ILE* 4.7 6.5 - - + -
2348C ASN 2.9 7.8 + - - +
2349C PHE* 3.3 33.4 - - + -
2350C ILE 3.0 23.2 + - - +
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Residues in contact with VAL2225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2205C ALA* 3.3 5.3 - - - +
2206C PHE* 2.9 37.7 + - + +
2208C TYR* 3.6 32.3 - - + -
2223C THR* 4.2 7.9 - - + -
2224C VAL* 1.3 75.7 - - - +
2226C LEU* 1.3 64.1 + - - +
2227C VAL* 3.4 14.7 + - + +
2242C PRO* 3.9 21.1 - - + -
2244C ILE* 4.6 3.6 - - + -
2350C ILE* 3.4 37.9 - - + +
2374C PHE* 4.2 6.3 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il